[gmx-users] Another question about position restraints - and water
baaden at smplinux.de
Tue Nov 27 18:00:53 CET 2001
first, thank you all for your answers, which were very helpful and
indeed exactly what I was looking for.
Now I came across another problem with position restraints. In
the particular case I am interested in I have a protein in a
bilayer with crystal water (residue name HOH) and "solvation"
water (residue name SOL).
As I am still in the equilibration phase, I would like to keep
the xtal water position restrained, but let the bilayer and
If I try this with the options
define = -DPOSRES_protein -DPOSRES_xtalhoh
solvent-optimization = SOL
constraints = all-bonds
in the mdp file, I get an error
Molecule starting at atomnr. 43821 can not be settled, step 0, time 10 (ps)
which concerns one of the SOL (!!) waters. If I remove the
-DPOSRES_xtalhoh definition the same job runs all right.
Maybe I did not correctly declare my xtal water position restraints ?
Here how the important part of the topology looks like:
[ molecules ]
; name number
And the posres_XTALHOH.itp looks like this:
[ position_restraints ]
; atom type fx fy fz
1 1 1000.0 1000.0 1000.0
Any clues ? I wonder whether solvent and crystal waters might get
mixed up ?
Thanks in advance,
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217
More information about the gromacs.org_gmx-users